AutoCloner

Multiple sequence alignment - TraesCS1B01G139300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS1B01G139300	chr1B	100.000	2411	0	0	1	2411	183211206	183213616	0.000000e+00	4453.0
1	TraesCS1B01G139300	chr3B	98.332	1439	23	1	3	1441	7283121	7281684	0.000000e+00	2523.0
2	TraesCS1B01G139300	chr3B	95.576	972	40	3	1441	2411	166839596	166840565	0.000000e+00	1554.0
3	TraesCS1B01G139300	chr3B	95.946	148	6	0	1294	1441	653680754	653680607	8.610000e-60	241.0
4	TraesCS1B01G139300	chr2D	95.668	1131	49	0	314	1444	413689703	413688573	0.000000e+00	1818.0
5	TraesCS1B01G139300	chr7B	95.679	972	39	3	1441	2411	432881310	432882279	0.000000e+00	1559.0
6	TraesCS1B01G139300	chr7B	95.469	971	42	2	1441	2411	150536174	150535206	0.000000e+00	1548.0
7	TraesCS1B01G139300	chr7B	100.000	56	0	0	1386	1441	495085022	495085077	1.180000e-18	104.0
8	TraesCS1B01G139300	chr7B	95.000	60	3	0	1382	1441	251152462	251152403	7.100000e-16	95.3
9	TraesCS1B01G139300	chr6B	95.469	971	42	2	1441	2411	223098565	223099533	0.000000e+00	1548.0
10	TraesCS1B01G139300	chr6B	95.366	971	43	2	1441	2411	426697485	426698453	0.000000e+00	1543.0
11	TraesCS1B01G139300	chr6B	98.420	633	10	0	809	1441	707945727	707946359	0.000000e+00	1114.0
12	TraesCS1B01G139300	chr6B	73.728	1454	345	34	5	1441	21180222	21181655	3.530000e-148	534.0
13	TraesCS1B01G139300	chr6B	97.222	72	2	0	1370	1441	362196194	362196265	3.260000e-24	122.0
14	TraesCS1B01G139300	chr5B	95.473	972	41	3	1441	2411	112517575	112516606	0.000000e+00	1548.0
15	TraesCS1B01G139300	chr5B	95.469	971	42	2	1441	2411	706440828	706439860	0.000000e+00	1548.0
16	TraesCS1B01G139300	chr2B	95.469	971	43	1	1441	2411	216397109	216398078	0.000000e+00	1548.0
17	TraesCS1B01G139300	chr4B	95.366	971	43	2	1441	2411	440596126	440595158	0.000000e+00	1543.0
18	TraesCS1B01G139300	chr7A	76.168	1456	314	30	3	1441	711304286	711305725	0.000000e+00	736.0
19	TraesCS1B01G139300	chr6A	75.275	1452	329	26	5	1437	469918908	469920348	0.000000e+00	665.0
20	TraesCS1B01G139300	chr6A	81.106	217	37	4	317	531	140031511	140031725	1.150000e-38	171.0
21	TraesCS1B01G139300	chr6A	81.106	217	37	4	317	531	140053653	140053867	1.150000e-38	171.0
22	TraesCS1B01G139300	chr3A	73.697	806	180	26	14	810	37348184	37347402	3.920000e-73	285.0
23	TraesCS1B01G139300	chr4A	92.481	133	10	0	1299	1431	718037960	718038092	8.800000e-45	191.0
24	TraesCS1B01G139300	chr4A	92.481	133	10	0	1299	1431	718143286	718143418	8.800000e-45	191.0
25	TraesCS1B01G139300	chr1D	73.245	527	129	11	317	837	492531434	492530914	5.290000e-42	182.0

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS1B01G139300	chr1B	183211206	183213616	2410	False	4453	4453	100.000	1	2411	1	chr1B.!!$F1	2410
1	TraesCS1B01G139300	chr3B	7281684	7283121	1437	True	2523	2523	98.332	3	1441	1	chr3B.!!$R1	1438
2	TraesCS1B01G139300	chr3B	166839596	166840565	969	False	1554	1554	95.576	1441	2411	1	chr3B.!!$F1	970
3	TraesCS1B01G139300	chr2D	413688573	413689703	1130	True	1818	1818	95.668	314	1444	1	chr2D.!!$R1	1130
4	TraesCS1B01G139300	chr7B	432881310	432882279	969	False	1559	1559	95.679	1441	2411	1	chr7B.!!$F1	970
5	TraesCS1B01G139300	chr7B	150535206	150536174	968	True	1548	1548	95.469	1441	2411	1	chr7B.!!$R1	970
6	TraesCS1B01G139300	chr6B	223098565	223099533	968	False	1548	1548	95.469	1441	2411	1	chr6B.!!$F2	970
7	TraesCS1B01G139300	chr6B	426697485	426698453	968	False	1543	1543	95.366	1441	2411	1	chr6B.!!$F4	970
8	TraesCS1B01G139300	chr6B	707945727	707946359	632	False	1114	1114	98.420	809	1441	1	chr6B.!!$F5	632
9	TraesCS1B01G139300	chr6B	21180222	21181655	1433	False	534	534	73.728	5	1441	1	chr6B.!!$F1	1436
10	TraesCS1B01G139300	chr5B	112516606	112517575	969	True	1548	1548	95.473	1441	2411	1	chr5B.!!$R1	970
11	TraesCS1B01G139300	chr5B	706439860	706440828	968	True	1548	1548	95.469	1441	2411	1	chr5B.!!$R2	970
12	TraesCS1B01G139300	chr2B	216397109	216398078	969	False	1548	1548	95.469	1441	2411	1	chr2B.!!$F1	970
13	TraesCS1B01G139300	chr4B	440595158	440596126	968	True	1543	1543	95.366	1441	2411	1	chr4B.!!$R1	970
14	TraesCS1B01G139300	chr7A	711304286	711305725	1439	False	736	736	76.168	3	1441	1	chr7A.!!$F1	1438
15	TraesCS1B01G139300	chr6A	469918908	469920348	1440	False	665	665	75.275	5	1437	1	chr6A.!!$F3	1432
16	TraesCS1B01G139300	chr3A	37347402	37348184	782	True	285	285	73.697	14	810	1	chr3A.!!$R1	796

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
670	674	1.00358	ACCAATGCACGGATGAGAAGT	59.996	47.619	10.93	0.0	0.0	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1830	1843	1.670295	GCATAATCATGTGGACACGCA	59.33	47.619	0.0	0.0	42.06	5.24	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
49	50	2.102588	GGAGAACAGGTGCGTATATGGT	59.897	50.000	0.00	0.00	0.00	3.55
555	556	1.783071	TGTATAGGTGTCCGATGGCA	58.217	50.000	0.00	0.00	0.00	4.92
647	651	2.360475	GTGGGCTCTTCACCTGCC	60.360	66.667	0.00	0.00	45.42	4.85
667	671	1.811965	CAAACCAATGCACGGATGAGA	59.188	47.619	10.93	0.00	0.00	3.27
670	674	1.003580	ACCAATGCACGGATGAGAAGT	59.996	47.619	10.93	0.00	0.00	3.01
784	788	4.380233	GCAGATTTTTGTGCAGCTACATCT	60.380	41.667	0.00	0.00	39.62	2.90
967	979	1.775039	ATTGAACATCGATGGCGCCG	61.775	55.000	28.09	10.43	37.46	6.46
1124	1136	0.613260	ATTTCCCTCACGCTAGCACA	59.387	50.000	16.45	0.00	0.00	4.57
1469	1482	4.826733	TGAAAAGAATGCTTTAGGTGCTGA	59.173	37.500	0.00	0.00	43.32	4.26
1501	1514	8.735692	TGTTGAATTCATTCATGATGCTACTA	57.264	30.769	9.40	0.00	45.30	1.82
1561	1574	9.822185	GGAATTGCAATAATATCAAGTTTCCTT	57.178	29.630	13.39	0.00	31.31	3.36
1793	1806	3.838120	AGGCATTAAAGAAAAGCGCTTC	58.162	40.909	25.24	12.58	0.00	3.86
1800	1813	1.239347	AGAAAAGCGCTTCTTGGGAC	58.761	50.000	25.24	9.64	34.67	4.46
1902	1915	9.606631	TTTTGTTTCAATAAAGTGCCAAGTAAT	57.393	25.926	0.00	0.00	0.00	1.89
1945	1958	5.419542	GTGATAGTTGTGTTGATCCTGCTA	58.580	41.667	0.00	0.00	0.00	3.49
1965	1978	7.172019	CCTGCTAAAAATCAGAAACTTTTGCAT	59.828	33.333	9.91	0.00	31.79	3.96
2316	2332	4.232221	CGGAGCTTACGAGTTTTCTGTTA	58.768	43.478	5.93	0.00	0.00	2.41

Showing 1 to 17 of 17 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.490490	ACACGCCACATGATCCCTTAT	59.510	47.619	0.00	0.00	0.00	1.73
1	2	0.908910	ACACGCCACATGATCCCTTA	59.091	50.000	0.00	0.00	0.00	2.69
49	50	1.008327	TCTAGGGAGCCAAGGATCACA	59.992	52.381	9.55	0.00	36.23	3.58
539	540	2.799126	TTTTGCCATCGGACACCTAT	57.201	45.000	0.00	0.00	0.00	2.57
647	651	1.811965	TCTCATCCGTGCATTGGTTTG	59.188	47.619	7.71	7.34	0.00	2.93
667	671	2.567169	TCATGATCACCGGAAGACACTT	59.433	45.455	9.46	0.00	0.00	3.16
670	674	1.135112	CGTCATGATCACCGGAAGACA	60.135	52.381	9.46	7.35	0.00	3.41
967	979	0.467804	GTGCCATCCTCTTCTCTCCC	59.532	60.000	0.00	0.00	0.00	4.30
1124	1136	3.097614	AGGATAAACGGCAGTGTAGTCT	58.902	45.455	0.00	0.00	0.00	3.24
1352	1365	3.640029	GCCAATTTCATCAGGTCCATGAT	59.360	43.478	0.00	0.00	40.59	2.45
1561	1574	6.371548	AGCTTCACGAATTTAAGCACATAGAA	59.628	34.615	14.31	0.00	46.35	2.10
1800	1813	8.519799	ACAGTAAGGATAAATATTGGGTTGTG	57.480	34.615	0.00	0.00	0.00	3.33
1830	1843	1.670295	GCATAATCATGTGGACACGCA	59.330	47.619	0.00	0.00	42.06	5.24
1831	1844	1.942657	AGCATAATCATGTGGACACGC	59.057	47.619	0.00	0.00	34.40	5.34
1832	1845	4.209911	CAGTAGCATAATCATGTGGACACG	59.790	45.833	0.00	0.00	34.40	4.49
1902	1915	4.467082	TCACCGTAAGCCATCCTAAAGTTA	59.533	41.667	0.00	0.00	0.00	2.24
1904	1917	2.835764	TCACCGTAAGCCATCCTAAAGT	59.164	45.455	0.00	0.00	0.00	2.66
1945	1958	7.049754	ACTGGATGCAAAAGTTTCTGATTTTT	58.950	30.769	0.00	0.00	0.00	1.94
2114	2128	7.979444	ACAGAATCTATCAAAAACGGAAGAA	57.021	32.000	0.00	0.00	0.00	2.52
2242	2258	9.522804	CTTAGGTACTGTAATGAACTCATTCTC	57.477	37.037	8.19	4.84	42.19	2.87
2316	2332	7.494298	ACTTGAAAACTTCACAACACAAAACTT	59.506	29.630	0.00	0.00	39.87	2.66

Showing 1 to 21 of 21 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.